Publications
78 results found
Delhaye G, van der Linde S, Bauman D, et al., 2024, Ectomycorrhizal fungi are influenced by ecoregion boundaries across Europe, Global Ecology and Biogeography, ISSN: 1466-822X
<jats:title>Abstract</jats:title><jats:sec><jats:title>Aim</jats:title><jats:p>Ecoregions and the distance decay in community similarity are fundamental concepts in biogeography and conservation biology that are well supported across plants and animals, but not fungi. Here we test the relevance of these concepts for ectomycorrhizal (ECM) fungi in temperate and boreal regions.</jats:p></jats:sec><jats:sec><jats:title>Location</jats:title><jats:p>Europe.</jats:p></jats:sec><jats:sec><jats:title>Time Period</jats:title><jats:p>2008–2015.</jats:p></jats:sec><jats:sec><jats:title>Major Taxa Studied</jats:title><jats:p>Ectomycorrhizal fungi.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We used a large dataset of ~24,000 ectomycorrhizas, assigned to 1350 operational taxonomic units, collected from 129 forest plots via a standardized protocol. We investigated the relevance of ecoregion delimitations for ECM fungi through complementary methodological approaches based on distance decay models, multivariate analyses and indicator species analyses. We then evaluated the effects of host tree and climate on the observed biogeographical distributions.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Ecoregions predict large‐scale ECM fungal biodiversity patterns. This is partly explained by climate differences between ecoregions but independent from host tree distribution. Basidiomycetes in the orders Russulales and Atheliales and producing epigeous fruiting bodies, with potentially short‐distance dispersal, show the best agreement with ecoregion boundaries. Host tree distribution and fungal abundance (as opposed to presence/absence only) are important to uncover biogeographical patterns in mycorrhizas.</jats:p>&l
Bellotto-Trigo FC, Uezu A, Hatfield JH, et al., 2023, Intraspecific variation in sensitivity to habitat fragmentation is influenced by forest cover and distance to the range edge, BIOLOGICAL CONSERVATION, Vol: 284, ISSN: 0006-3207
Tan C, Trew J, Peacock T, et al., 2023, Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential, Nature Communications, Vol: 14, Pages: 1-13, ISSN: 2041-1723
There has been limited characterisation of bat-borne coronaviruses in Europe. Here, we screened for coronaviruses in 48 faecal samples from 16 of the 17 bat species breeding in the UK, collected through a bat rehabilitation and conservationist network. We recovered nine (two novel) complete genomes across six bat species: four alphacoronaviruses, a MERS-related betacoronavirus, and four closely related sarbecoviruses. We demonstrate that at least one of these sarbecoviruses can bind and use the human ACE2 receptor for infecting human cells, albeit suboptimally. Additionally, the spike proteins of these sarbecoviruses possess an R-A-K-Q motif, which lies only one nucleotide mutation away from a furin cleavage site (FCS) that enhances infectivity in other coronaviruses, including SARS-CoV-2. However, mutating this motif to an FCS does not enable spike cleavage. Overall, while UK sarbecoviruses would require further molecular adaptations to infect humans, their zoonotic risk is unknown and warrants closer surveillance.
Banks-Leite C, Betts MG, Ewers RM, et al., 2022, The macroecology of landscape ecology, Trends in Ecology and Evolution, Vol: 37, ISSN: 0169-5347
One of landscape ecology's main goals is to unveil how biodiversity is impacted by habitat transformation. However, the discipline suffers from significant context dependency in observed spatial and temporal trends, hindering progress towards understanding the mechanisms driving species declines and preventing the development of accurate estimates of future biodiversity change. Here, we discuss recent evidence that populations' and species' responses to habitat change at the landscape scale are modulated by factors and processes occurring at macroecological scales, such as historical disturbance rates, distance to geographic range edges, and climatic suitability. We suggest that placing landscape ecology studies in a macroecological lens will help to explain seemingly inconsistent results and will ultimately create better predictive models to help mitigate the biodiversity crisis.
Heath R, Orme DS, Sethi CSL, et al., 2021, How index selection, compression, and recording schedule impact the description of ecological soundscapes, Evolutionary Ecology, Vol: 11, Pages: 13206-13217, ISSN: 0269-7653
Acoustic indices derived from environmental soundscape recordings are being used to monitor ecosystem health and vocal animal biodiversity. Soundscape data can quickly become very expensive and difficult to manage, so data compression or temporal down-sampling are sometimes employed to reduce data storage and transmission costs. These parameters vary widely between experiments, with the consequences of this variation remaining mostly unknown.We analyse field recordings from North-Eastern Borneo across a gradient of historical land use. We quantify the impact of experimental parameters (MP3 compression, recording length and temporal subsetting) on soundscape descriptors (Analytical Indices and a convolutional neural net derived AudioSet Fingerprint). Both descriptor types were tested for their robustness to parameter alteration and their usability in a soundscape classification task.We find that compression and recording length both drive considerable variation in calculated index values. However, we find that the effects of this variation and temporal subsetting on the performance of classification models is minor: performance is much more strongly determined by acoustic index choice, with Audioset fingerprinting offering substantially greater (12%–16%) levels of classifier accuracy, precision and recall.We advise using the AudioSet Fingerprint in soundscape analysis, finding superior and consistent performance even on small pools of data. If data storage is a bottleneck to a study, we recommend Variable Bit Rate encoded compression (quality = 0) to reduce file size to 23% file size without affecting most Analytical Index values. The AudioSet Fingerprint can be compressed further to a Constant Bit Rate encoding of 64 kb/s (8% file size) without any detectable effect. These recommendations allow the efficient use of restricted data storage whilst permitting comparability of results between different studies.
Eyres A, Boehning-Gaese K, Orme CDL, et al., 2020, A tale of two seasons: The link between seasonal migration and climatic niches in passerine birds, ECOLOGY AND EVOLUTION, Vol: 10, Pages: 11983-11997, ISSN: 2045-7758
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- Citations: 7
Sethi S, Ewers R, Jones N, et al., 2020, SAFE Acoustics: an open-source, real-time eco-acoustic monitoring network in the tropical rainforests of Borneo, Methods in Ecology and Evolution, Vol: 11, Pages: 1182-1185, ISSN: 2041-210X
1. Automated monitoring approaches offer an avenue to unlocking large‐scale insight into how ecosystems respond to human pressures. However, since data collection and data analyses are often treated independently, there are currently no open‐source examples of end‐to‐end, real‐time ecological monitoring networks. 2. Here, we present the complete implementation of an autonomous acoustic monitoring network deployed in the tropical rainforests of Borneo. Real‐time audio is uploaded remotely from the field, indexed by a central database, and delivered via an API to a public‐facing website.3. We provide the open‐source code and design of our monitoring devices, the central web2py database, and the ReactJS website. Furthermore, we demonstrate an extension of this infrastructure to deliver real‐time analyses of the eco‐acoustic data. 4. By detailing a fully functional, open source, and extensively tested design, our work will accelerate the rate at which fully autonomous monitoring networks mature from technological curiosities, and towards genuinely impactful tools in ecology.
Sethi S, Jones NS, Fulcher B, et al., 2020, Characterising soundscapes across diverse ecosystems using a universal acoustic feature set, Proceedings of the National Academy of Sciences of USA, Vol: 117, Pages: 17049-17055, ISSN: 0027-8424
Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labor-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we have developed a generalizable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed soundscapes from a variety of ecosystems into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, providing a potential route for real-time automated detection of irregular environmental behavior including illegal logging and hunting. Our highly generalizable approach, and the common set of features, will enable scientists to unlock previously hidden insights from acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.
Sarab S, Orme C, 2020, sarabsethi/rpi-eco-monitoring: Release for SAFE Acoustics publication
Software for long-term autonomous ecosystem monitoring on a Raspberry Pi
Hatfield J, Barlow J, Joly CA, et al., 2020, Mediation of area and edge effects by adjacent land use, Conservation Biology, Vol: 34, Pages: 395-404, ISSN: 0888-8892
Habitat loss, fragmentation and degradation have pervasive detrimental effects on tropical forest biodiversity, but the role of the surrounding land use (i.e. matrix) in determining the severity of these impacts remains poorly understood. We surveyed bird species across an interior-edge-matrix gradient to assess the effects of matrix type on biodiversity at 49 different sites with varying levels of landscape fragmentation in the Brazilian Atlantic Forest – a highly threatened biodiversity hotspot. Our findings revealed that both area and edge effects are more pronounced in forest patches bordering pasture matrix, while patches bordering Eucalyptus plantation maintained compositionally similar bird communities between the edge and the interior, in addition to exhibiting reduced effects of patch size. These results suggest that the type of matrix in which forest fragments are situated can explain a substantial amount of the widely-reported variability in biodiversity responses to forest loss and fragmentation.
Sethi SS, Ewers RM, Jones NS, et al., 2020, SAFE Acoustics: an open-source, real-time eco-acoustic monitoring network in the tropical rainforests of Borneo
<jats:title>Abstract</jats:title><jats:p><jats:list list-type="order"><jats:list-item><jats:p>Automated monitoring approaches offer an avenue to deep, large-scale insight into how ecosystems respond to human pressures. Since sensor technology and data analyses are often treated independantly, there are no open-source examples of end-to-end, real-time ecological monitoring networks.</jats:p></jats:list-item><jats:list-item><jats:p>Here, we present the complete implementation of an autonomous acoustic monitoring network deployed in the tropical rainforests of Borneo. Real-time audio is uploaded remotely from the field, indexed by a central database, and delivered via an API to a public-facing website.</jats:p></jats:list-item><jats:list-item><jats:p>We provide the open-source code and design of our monitoring devices, the central web2py database and the ReactJS website. Furthermore, we demonstrate an extension of this infrastructure to deliver real-time analyses of the eco-acoustic data.</jats:p></jats:list-item><jats:list-item><jats:p>By detailing a fully functional, open-source, and extensively tested design, our work will accelerate the rate at which fully autonomous monitoring networks mature from technological curiosities, and towards genuinely impactful tools in ecology.</jats:p></jats:list-item></jats:list></jats:p>
Betts MG, Wolf C, Pfeifer M, et al., 2019, Extinction filters mediate the global effects of habitat fragmentation on animals, Science, Vol: 366, Pages: 1236-1239, ISSN: 0036-8075
Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity-affected by avoidance of habitat edges-should be driven by historical exposure to, and therefore species' evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world's tropical forests.
Sethi S, Jones N, Fulcher B, et al., 2019, Combining machine learning and a universal acoustic feature-set yields efficient automated monitoring of ecosystems, Publisher: bioRxiv
Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labour-intensive surveys that are unable to detect rapid or unanticipated environmental changes. Here we developed a generalisable, data-driven solution to this challenge using eco-acoustic data. We exploited a convolutional neural network to embed ecosystem soundscapes from a wide variety of biomes into a common acoustic space. In both supervised and unsupervised modes, this allowed us to accurately quantify variation in habitat quality across space and in biodiversity through time. On the scale of seconds, we learned a typical soundscape model that allowed automatic identification of anomalous sounds in playback experiments, paving the way for real-time detection of irregular environmental behaviour including illegal activity. Our highly generalisable approach, and the common set of features, will enable scientists to unlock previously hidden insights from eco-acoustic data and offers promise as a backbone technology for global collaborative autonomous ecosystem monitoring efforts.
Orme CDL, Mayor S, Dos Anjos L, et al., 2019, Publisher Correction: Distance to range edge determines sensitivity to deforestation, Nature Ecology and Evolution, Vol: 3, Pages: 1131-1131, ISSN: 2397-334X
Correction to: Nature Ecology & Evolution https://doi.org/10.1038/s41559-019-0889-z, published online 06 May 2019.
Orme D, Mayor S, dos Anjos L, et al., 2019, Distance to range edge determines sensitivity to deforestation, Nature Ecology and Evolution, Vol: 3, Pages: 886-891, ISSN: 2397-334X
It is generally assumed that deforestation affects a species consistently across space, however populations near their geographic range edge may exist at their niche limits and therefore be more sensitive to disturbance. We found that both within and across Atlantic Forest bird species, populations are more sensitive to deforestation when near their range edge. In fact, the negative effects of deforestation on bird occurrences switched to positive in the range core (>829 km), in line with Ellenberg’s rule. We show that the proportion of populations at their range core and edge varies across Brazil, suggesting deforestation effects on communities, and hence the most appropriate conservation action, also vary geographically.
Sethi S, Ewers R, Jones N, et al., 2018, Robust, real-time and autonomous monitoring of ecosystems with an open, low-cost, networked device, Methods in Ecology and Evolution, Vol: 9, Pages: 2383-2387, ISSN: 2041-210X
1. Automated methods of monitoring ecosystems provide a cost-effective way to track changes in natural system's dynamics across temporal and spatial scales. However, methods of recording and storing data captured from the field still require significant manual effort. 2. Here we introduce an open source, inexpensive, fully autonomous ecosystem monitoring unit for capturing and remotely transmitting continuous data streams from field sites over long time-periods. We provide a modular software framework for deploying various sensors, together with implementations to demonstrate proof of concept for continuous audio monitoring and time-lapse photography. 3. We show how our system can outperform comparable technologies for fractions of the cost, provided a local mobile network link is available. The system is robust to unreliable network signals and has been shown to function in extreme environmental conditions, such as in the tropical rainforests of Sabah, Borneo. 4. We provide full details on how to assemble the hardware, and the open-source software. Paired with appropriate automated analysis techniques, this system could provide spatially dense, near real-time, continuous insights into ecosystem and biodiversity dynamics at a low cost.
Hatfield JH, Orme CDL, Banks-Leite C, 2018, Using functional connectivity to predict potential meta-population sizes in the Brazilian Atlantic Forest, Perspectives in Ecology and Conservation, Vol: 16, Pages: 215-220, ISSN: 2530-0644
Habitat loss and fragmentation reduce population sizes and increase isolation between populations. To better understand how functional connectivity is affected by habitat modification over large scales, we here applied a meta-population framework to the Brazilian Atlantic Forest, a highly degraded and fragmented biodiversity hotspot. Other studies have used mainly hypothetical or estimated dispersal values for connectivity calculation which may not be reflective of species requirements. Here, we collated dispersal values for 45 species of birds, 5 mammals and 4 insects and found that 50% of the Atlantic Forest species can cross only up to 150 m of open gaps between forest patches. Because of the high levels of fragmentation, the median size of a functionally connected network of fragments in the Brazilian Atlantic Forest only decreased from 15 ha to 14 ha when the crossable distance considered was reduced from 150 m to 0 m. We show that for species solely reliant on native forest habitat, a large proportion of the remaining Atlantic Forest fragments represent many small and isolated populations with few large connected areas. Our results support further evidence that for future management and restoration to be successful, existing connectivity must be vastly improved to provide forest areas large enough to support viable populations.
van der Linde S, Suz LM, Orme CDL, et al., 2018, Author Correction: Environment and host as large-scale controls of ectomycorrhizal fungi., Nature
In the HTML version of this Article, author 'Filipa Cox' had no affiliation in the author list, although she was correctly associated with affiliation 3 (Earth & Environmental Sciences, University of Manchester, Manchester, UK) in the PDF. In addition, the blue circles for 'oak' were missing from Extended Data Fig. 1. These errors have been corrected online.
van der Linde S, Suz LM, Orme CDL, et al., 2018, Environment and host as large-scale controls of ectomycorrhizal fungi, Nature, Vol: 558, Pages: 243-248, ISSN: 0028-0836
Explaining the large-scale diversity of soil organisms that drive biogeochemical processes-and their responses to environmental change-is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is-to our knowledge-unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.
Roll U, Feldman A, Novosolov M, et al., 2018, The global distribution of tetrapods reveals a need for targeted reptile conservation (vol 1, pg 1677, 2017), NATURE ECOLOGY & EVOLUTION, Vol: 2, Pages: 193-193, ISSN: 2397-334X
Sethi SS, Ewers RM, Jones NS, et al., 2017, Robust, real-time and autonomous monitoring of ecosystems with an open, low-cost, networked device
<jats:title>Abstract</jats:title><jats:p><jats:list list-type="order"><jats:list-item><jats:p>Automated methods of monitoring ecosystems provide a cost-effective way to track changes in natural system’s dynamics across temporal and spatial scales. However, methods of recording and storing data captured from the field still require significant manual effort.</jats:p></jats:list-item><jats:list-item><jats:p>Here we introduce an open source, inexpensive, fully autonomous ecosystem monitoring unit for capturing and remotely transmitting continuous data streams from field sites over long time-periods. We provide a modular software framework for deploying various sensors, together with implementations to demonstrate proof of concept for continuous audio monitoring and time-lapse photography.</jats:p></jats:list-item><jats:list-item><jats:p>We show how our system can outperform comparable technologies for fractions of the cost, provided a local mobile network link is available. The system is robust to unreliable network signals and has been shown to function in extreme environmental conditions, such as in the tropical rainforests of Sabah, Borneo.</jats:p></jats:list-item><jats:list-item><jats:p>We provide full details on how to assemble the hardware, and the open-source software. Paired with appropriate automated analysis techniques, this system could provide spatially dense, near real-time, continuous insights into ecosystem and biodiversity dynamics at a low cost.</jats:p></jats:list-item></jats:list></jats:p>
Roll U, Feldman A, Novosolov M, et al., 2017, The global distribution of tetrapods reveals a need for targeted reptile conservation, NATURE ECOLOGY & EVOLUTION, Vol: 1, Pages: 1677-1682, ISSN: 2397-334X
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- Citations: 320
Roll U, Feldman A, Novosolov M, et al., 2017, The global distribution of tetrapods reveals a need for targeted reptile conservation (vol 1, pg 1677, 2017), NATURE ECOLOGY & EVOLUTION, Vol: 1, Pages: 1785-1785, ISSN: 2397-334X
Hatfield JH, Orme CDL, Tobias JA, et al., 2017, Trait-based indicators of bird species sensitivity to habitat loss are effective within but not across datasets., Ecological Applications, Vol: 28, Pages: 28-34, ISSN: 1051-0761
Species' traits have been widely championed as the key to predicting which species are most threatened by habitat loss, yet previous work has failed to detect trends that are consistent enough to guide large-scale conservation and management. Here we explore whether traits and environmental variables predict species sensitivity to habitat loss across two datasets generated by independent avifaunal studies in the Atlantic Forest of Brazil, both of which detected a similar assemblage of species, and similar species-specific responses to habitat change, across an overlapping sample of sites. Specifically, we tested whether 25 distributional, climatic, ecological, behavioral and morphological variables predict sensitivity to habitat loss among 196 bird species, both within and across studies, and when data were analysed as occurrence or abundance. We found that 4-9 variables showed high explanatory power within a single study or dataset, but none performed as strong predictors across all datasets. Our results demonstrate that the use of species traits to predict sensitivity to anthropogenic habitat loss can produce predictions that are species- and site-specific and not scalable to whole regions or biomes, and thus should be used with caution. This article is protected by copyright. All rights reserved.
Bland LM, Bielby J, Kearney S, et al., 2017, Toward reassessing data-deficient species, CONSERVATION BIOLOGY, Vol: 31, Pages: 531-539, ISSN: 0888-8892
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- Citations: 54
Dyer EE, Cassey P, Redding DW, et al., 2017, The Global Distribution and Drivers of Alien Bird Species Richness, PLOS BIOLOGY, Vol: 15, ISSN: 1545-7885
Tang CQ, Orme CDL, Bunnefeld L, et al., 2016, Global monocot diversification: geography better explains variation in species richness than environment or biology, Botanical Journal of the Linnean Society, Vol: 183, Pages: 1-15, ISSN: 0024-4074
Monocots account for a quarter of angiosperm species richness and are among the most economically and culturally important plants, including cereals (grasses), palms, orchids and lilies. Previous investigations of correlates of monocot species diversity have varied in scale and usually concentrated on a few drivers of diversification. Here, to disentangle the correlates of monocot diversity, we reconstructed a genus-level phylogenetic tree (1987 of the 2713 genera) and compiled an extensive database of abiotic, biotic and geographical characteristics to assess whether differences in these traits correlate with the vast asymmetrical species richness among genera present in this clade. Our results support several classical biodiversity theories, including species–area relationships, and latitudinal and elevational diversity gradients. Furthermore, interactions among these factors explain an additional 10% of the variation (compared to 36% from the main effects alone). We conclude that higher species richness among monocot genera is associated with geographical variables, especially larger ranges and lower elevations, rather than physical environment or physiology.
Oliver TH, Heard MS, Isaac NJB, et al., 2016, A Synthesis is Emerging between Biodiversity-Ecosystem Function and Ecological Resilience Research: Reply to Mori, TRENDS IN ECOLOGY & EVOLUTION, Vol: 31, Pages: 89-92, ISSN: 0169-5347
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- Citations: 17
Oliver TH, Heard MS, Isaac NJB, et al., 2015, Biodiversity and Resilience of Ecosystem Functions., Trends Ecol Evol, Vol: 30, Pages: 673-684
Accelerating rates of environmental change and the continued loss of global biodiversity threaten functions and services delivered by ecosystems. Much ecosystem monitoring and management is focused on the provision of ecosystem functions and services under current environmental conditions, yet this could lead to inappropriate management guidance and undervaluation of the importance of biodiversity. The maintenance of ecosystem functions and services under substantial predicted future environmental change (i.e., their 'resilience') is crucial. Here we identify a range of mechanisms underpinning the resilience of ecosystem functions across three ecological scales. Although potentially less important in the short term, biodiversity, encompassing variation from within species to across landscapes, may be crucial for the longer-term resilience of ecosystem functions and the services that they underpin.
Bland LM, Orme CDL, Bielby J, et al., 2015, Cost-effective assessment of extinction risk with limited information, JOURNAL OF APPLIED ECOLOGY, Vol: 52, Pages: 861-870, ISSN: 0021-8901
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- Citations: 35
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